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The Journal of General and Applied... 2020
Topics: Biotechnology; Cyanobacteria; Ecology; Microalgae; Microbiology; Molecular Biology
PubMed: 32554950
DOI: 10.2323/jgam.2020.04.001 -
ELife Feb 2021Integrating the analysis of molecular data from different sources may improve our understanding of the effects of biological aging.
Integrating the analysis of molecular data from different sources may improve our understanding of the effects of biological aging.
Topics: Genomics; Metabolomics; Proteomics
PubMed: 33576740
DOI: 10.7554/eLife.66223 -
Molecular Imaging and Biology Feb 2020
Topics: Awards and Prizes; Biology; Canada; Congresses as Topic; Humans; International Agencies; Molecular Imaging
PubMed: 31667716
DOI: 10.1007/s11307-019-01444-0 -
Journal of Translational Medicine Jul 2023Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA)... (Review)
Review
Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses computational models to perform complex experiments that are otherwise prohibitively expensive or require a microgravity environment. Similarly, the Food and Drug Administration (FDA) and European Medicines Agency (EMA) have began accepting models and simulations as forms of evidence for pharmaceutical and medical device approval. It is crucial that computational models meet a standard of credibility when using them in high-stakes decision making. For this reason, institutes including NASA, the FDA, and the EMA have developed standards to promote and assess the credibility of computational models and simulations. However, due to the breadth of models these institutes assess, these credibility standards are mostly qualitative and avoid making specific recommendations. On the other hand, modeling and simulation in systems biology is a narrower domain and several standards are already in place. As systems biology models increase in complexity and influence, the development of a credibility assessment system is crucial. Here we review existing standards in systems biology, credibility standards in other science, engineering, and medical fields, and propose the development of a credibility standard for systems biology models.
Topics: Systems Biology; Computer Simulation; Computational Biology
PubMed: 37496031
DOI: 10.1186/s12967-023-04290-5 -
Molecular Systems Biology Jan 2012Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have typically been... (Review)
Review
Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have typically been generated under a single condition, even though biological systems undergo differential change that is dependent on environment, tissue type, disease state, development or speciation. Several recent interaction mapping studies have demonstrated the power of differential analysis for elucidating fundamental biological responses, revealing that the architecture of an interactome can be massively re-wired during a cellular or adaptive response. Here, we review the technological developments and experimental designs that have enabled differential network mapping at very large scales and highlight biological insight that has been derived from this type of analysis. We argue that differential network mapping, which allows for the interrogation of previously unexplored interaction spaces, will become a standard mode of network analysis in the future, just as differential gene expression and protein phosphorylation studies are already pervasive in genomic and proteomic analysis.
Topics: Animals; Biology; Epistasis, Genetic; Gene Regulatory Networks; Genes, Essential; Humans; Matched-Pair Analysis; Models, Biological; Protein Interaction Maps; Systems Biology
PubMed: 22252388
DOI: 10.1038/msb.2011.99 -
Cytometry. Part a : the Journal of the... Oct 2020The advent of modern "omics" technologies (genomics, transcriptomics, proteomics, and metabolomics) are attributed to innovative breakthroughs in genome sequencing,... (Review)
Review
The advent of modern "omics" technologies (genomics, transcriptomics, proteomics, and metabolomics) are attributed to innovative breakthroughs in genome sequencing, bioinformatics, and analytic tools. An organism's biological structure and function is the result of the concerted action of single cells in different tissues. Single cell genomics has emerged as a ground-breaking technology that has greatly enhanced our understanding of the complexity of gene expression at a microscopic resolution and holds the potential to revolutionize the way we characterize complex cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and networking. Mammalian systems have benefitted immensely from these approaches to dissect complex systems such as cancer, immunological disorders, epigenetic controls of diseases, and understanding of developmental biology. However, the applications of single-cell omics in plant research are just starting. The potential to decipher the fundamentals of developmental and functional biology of large and complex plant species at the single-cell resolution are now becoming important drivers of research. In this review, we present the status, challenges and potential of one important and most commonly used single-cell omics technique in plants, namely single cell transcriptomics. © 2020 International Society for Advancement of Cytometry.
Topics: Animals; Computational Biology; Genomics; Metabolomics; Plant Development; Transcriptome
PubMed: 32713117
DOI: 10.1002/cyto.a.24196 -
Molecules (Basel, Switzerland) May 2021In the natural environment, interactions between species are a common natural phenomena. The mechanisms of interaction between different species are mainly studied using... (Review)
Review
In the natural environment, interactions between species are a common natural phenomena. The mechanisms of interaction between different species are mainly studied using genomic, transcriptomic, proteomic, and metabolomic techniques. Metabolomics is a crucial part of system biology and is based on precision instrument analysis. In the last decade, the emerging field of metabolomics has received extensive attention. Metabolomics not only provides a qualitative and quantitative method for studying the mechanisms of interactions between different species, but also helps clarify the mechanisms of defense between the host and pathogen, and to explore new metabolites with various biological activities. This review focuses on the methods and progress of interspecies metabolomics. Additionally, the prospects and challenges of interspecies metabolomics are discussed.
Topics: Computational Biology; Gene Expression Profiling; Genomics; Host-Pathogen Interactions; Metabolomics; Proteomics; Species Specificity
PubMed: 34072976
DOI: 10.3390/molecules26113311 -
FEMS Microbiology Reviews Jan 2009
Topics: Microbiology; Systems Biology
PubMed: 19054117
DOI: 10.1111/j.1574-6976.2008.00147.x -
Methods in Molecular Biology (Clifton,... 2011There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small... (Review)
Review
There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.
Topics: Biology; Computational Biology; Computer Simulation; Humans; Research; Systems Biology
PubMed: 20838980
DOI: 10.1007/978-1-60761-839-3_18 -
Methods in Molecular Biology (Clifton,... 2020Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for... (Review)
Review
Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.
Topics: Genomics; History, 20th Century; History, 21st Century; Humans; Ion Mobility Spectrometry; Metabolomics; Proteomics
PubMed: 31729651
DOI: 10.1007/978-1-0716-0030-6_1